The simple loop conjecture places very strong restrictions on the way a closed surface can map into a 3-manifold. Even if true, however, there are difficulties in constructing an algorithm to verify that any given map of a surface satisfies the conjecture. This has to do with the observation that certain questions about regular covers of surface groups are undecidable.
Links:
[1] http://www.mpim-bonn.mpg.de/taxonomy/term/39
[2] http://www.mpim-bonn.mpg.de/node/3444
[3] http://www.mpim-bonn.mpg.de/node/158